---
name: "xtractore"
section: "1"
platform: "linux"
package: "aegean"
version: "0.16.0+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/xtractore"
---

# xtractore(1)

extract sequences corresponding to annotated features from the given sequence file

## NAME

xtractore - extract sequences corresponding to annotated features from the given sequence file

## SYNOPSIS

**xtractore** \[*options*\] *features.gff3 sequences.fasta*

## DESCRIPTION

Options:

- **-d**\|--debug

  print debugging output

- **-h**\|--help

  print this help message and exit

- **-i**\|--idfile: FILE

  file containing a list of feature IDs (1 per line with no spaces); if provided, only features with IDs in this file will be extracted

- **-o**\|--outfile: FILE

  file to which output sequences will be written; default is terminal (stdout)

- **-t**\|--type: STRING

  feature type to extract; can be used multiple times to extract features of multiple types

- **-v**\|--version

  print version number and exit

- **-V**\|--verbose

  print verbose warning and error messages

- **-w**\|--width: INT

  width of each line of sequence in the Fasta output; default is 80; set to 0 for no formatting